This window displays all open reading frames of the loaded sequence. They are displayed graphically on the top and by the amino acid symbols on the bottom part of the window. The toolbar is located just below the sequence file name and contains the following elements:
• The zoom in and out slide bar to accurately control the size of the graphic display.
• The Options icon allowing for changing meaning of the colors. By default, the codon frequencies are displayed in various colors, but you may change this to amino acid type, where acidic amino acids are labeled in red, basic in blue, hydrophobic and aromatic in brown, nucleophilic (small) in black, cysteine in yellow and proline in green.
• The minimum size of an open reading frame that this window displays can be changed by typing the number on the “Min. ORF Size” box. Typing a larger number will eliminate short ORFs from the display, thus somewhat cleaning up the window.
• The cursor position is displayed at the right. The bottom window indicates this position by a vertical grey line.
ORFs are displayed graphically below the tool bar. The yellow line dividing the positive and negative strand ORFs has a green box representing the range of the lower portion of the window with amino acid symbols and the DNA sequence. The boundaries of the zoomed graph is indicated by the nucleotide numbers inside the graph area.
If you click on any of the ORF, displayed graphically or by the letters (the given ORF block is underlined in bright green) the ORF Statistics table will show its reading frame number, positions on the DNA sequence, size of the protein in the number of amino acids and molecular weight, as well as the mean pKa value, that is usually close to its isoelectric point.
To the right of the ORF Statistics table there is a table explaining the meaning of colors used to present ORFs in the graphic style (above) as well as in the letter style in the zoomed area below.
In the zoomed area at the bottom of the window you can see the DNA sequence in the middle, above it - its translation of the positive strand, and below the translation of its negative strand in all reading frames. The amino- and carboxy- termini of the proteins are labeled on the sides. The scale on the top indicates the nucleotide position of the sequence.